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767
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News:
Ensembl 113 has been released
ensembl
ensembldb
mart
biomaRt
11 months ago
Ensembl_Jorge
• 0
1
vote
9
replies
3.7k
views
Error using champ.import
ChAMP
EPICv2
updated 11 months ago by
Ricky
• 0 • written 2.2 years ago by
medha.suman
• 0
0
votes
1
reply
382
views
enrichKEGG
keggorthology
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
strawberry3
• 0
0
votes
3
replies
1.5k
views
Label specific rows in pheatmap
heatmaps
pheatmap
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Dina
▴ 50
3
votes
4
replies
2.4k
views
News:
Bioconductor 3.20 Release Schedule
software
release
Release
updated 4 months ago by
randyprice13102000
• 0 • written 12 months ago by
shepherl
4.2k
1
vote
2
replies
647
views
edgeR 4.2.2 not compiled for Windows
edger
edgeR
11 months ago
Hongjian
• 0
0
votes
1
reply
339
views
2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
11 months ago
JY
• 0
0
votes
1
reply
415
views
How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 11 months ago by
Michael Love
43k • written 11 months ago by
agamemnon
• 0
0
votes
2
replies
454
views
how to extract expression matrix post deseq2
DESeq2
written 11 months ago by
agamemnon
• 0
2
votes
2
replies
792
views
Automatically generate contrasts from a model matrix / formula
limma
updated 11 months ago by
ATpoint
★ 4.9k • written 11 months ago by
Jonathan
▴ 10
0
votes
2
replies
485
views
Using Normalized Counts in DESeq2
DESeq2
updated 11 months ago by
Michael Love
43k • written 11 months ago by
KokiBio
• 0
0
votes
0
replies
276
views
DiffBind subset replicates
DiffBind
11 months ago
Haiping
• 0
1
vote
3
replies
870
views
How to reverse complement some elements of a DNAStringSet
biostr
Biostrings
updated 5 months ago by
shrill.asp.tufl
• 0 • written 11 months ago by
Christine Jones
• 0
3
votes
2
replies
550
views
When running contrasts, does it use normalized read counts?
DESeq2
11 months ago
Katherine
▴ 20
0
votes
0
replies
389
views
Rsubread - sublong function
pacbio
sublong
Rsubread
11 months ago
thomas.heigl.ibk
• 0
3
votes
4
replies
1.4k
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata
Normalization_method
WGCNA
11 months ago
sukeshinik5
▴ 20
1
vote
3
replies
1.6k
views
featureCounts fails to load annotation file
featurecounts
rnas
RNASeqPower
11 months ago
yasmin.hilliam
▴ 10
0
votes
1
reply
387
views
How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 11 months ago by
swbarnes2
★ 1.4k • written 11 months ago by
Bingqian
• 0
1
vote
2
replies
711
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata
Biostrings
updated 9 months ago by
Aidan
▴ 70 • written 11 months ago by
Gerhard Thallinger
▴ 180
3
votes
3
replies
662
views
How to subset voomLmFit (MArrayLM) object?
limma
edgeR
11 months ago
Guido Hooiveld
★ 4.1k
0
votes
3
replies
684
views
Need help interpreting heatmaps from limma
limma
written 11 months ago by
lhwh1208
• 0
0
votes
0
replies
271
views
when FOLD>0, which group of sampls increased?
BASiCS
11 months ago
Jeffcgen2000
• 0
3
votes
4
replies
1.1k
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization
DESeq2
rlog
vst
11 months ago
Eva
▴ 10
1
vote
3
replies
4.0k
views
Unable to install any Bioconductor package with new R 4.4.1 - path nor writable - PLEASE HELP
pathnotwritable
BiocManager
LEA
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
gabry.scata
▴ 10
0
votes
0
replies
272
views
Paired splsda
mixOmics
11 months ago
michelafrancesconi8
• 0
2
votes
1
reply
1.9k
views
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
limma
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
danphillips28
▴ 10
0
votes
0
replies
520
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
11 months ago
Young Boqin
• 0
0
votes
0
replies
499
views
News:
Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment
SingleCell
11 months ago
info
▴ 10
4
votes
4
replies
706
views
How to conduct maSigPro analysis with only one condition?
maSigPro
masig
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Jiahao Tian
• 0
1
vote
4
replies
1.2k
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq
DESeq2
Oddresults
updated 11 months ago by
ATpoint
★ 4.9k • written 11 months ago by
Ricardo Iván
• 0
0
votes
1
reply
465
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression
ImpulseDE2
DESeq2
updated 11 months ago by
Michael Love
43k • written 11 months ago by
Jiahao Tian
• 0
0
votes
0
replies
411
views
DMRcate pcutoff setting
EpicV2
DMRcate
11 months ago
kitzhu
• 0
2
votes
4
replies
794
views
RNASeq Time Course Question
DESeq2
RNASeq
TimeCourse
11 months ago
jihoon.kim.1495
▴ 10
0
votes
0
replies
374
views
[maser] Why does maser coverage filtering ignore skipping counts of an alt. splicing analysis?
rMATS
alternativesplicing
maser
R
11 months ago
Anke
• 0
0
votes
6
replies
1.3k
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression
DESeq2
BatchEffect
updated 10 months ago by
Michael Love
43k • written 11 months ago by
CriticalPeriod
• 0
1
vote
1
reply
805
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 11 months ago by
Lluís Revilla Sancho
▴ 760 • written 11 months ago by
Nasim
• 0
5
votes
4
replies
923
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 11 months ago by
ATpoint
★ 4.9k • written 11 months ago by
Bioinformagician
• 0
4
votes
1
reply
606
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger
edgeR
updated 11 months ago by
Gordon Smyth
53k • written 11 months ago by
Hongjian
• 0
2
votes
5
replies
944
views
dmpFinder for other objects
methylset
minfi
dmpFinder
betaHMM
beta
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
neyousha
• 0
0
votes
1
reply
420
views
Unevaluated error in ChIPQC combined with BiocParallel
BiocParallel
ChIPQC
written 11 months ago by
Young Boqin
• 0
0
votes
2
replies
597
views
RNA-Seq p value range variation
DESeq2
pvalue
RNA-Seq
11 months ago
paul.meraner
• 0
0
votes
0
replies
506
views
News:
RNAseq data analysis with Bioconductor (online course)
DESeq2
SummarizedExperiment
11 months ago • updated 10 months ago
info
▴ 10
2
votes
8
replies
1.7k
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 9 months ago by
mercedeh.movassagh
▴ 20 • written 18 months ago by
María Calvo
• 0
1
vote
6
replies
1.3k
views
heatmap with batch effect
DESeq2
BatchEffect
written 11 months ago by
tothuhien
• 0
0
votes
1
reply
496
views
how do I convert an Ilumn IDREF to a CPG loci
AnnotationDbi
Annotation
annotation
BiologicalQuestion
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Olajumoke
• 0
0
votes
1
reply
610
views
Setting ylims in bam coverage plot and assigning compound sashimi numbers to overlay plots
Coverage
Gviz
sashimi
updated 4 months ago by
macdonaldfrench7286566
• 0 • written 11 months ago by
Marco
• 0
0
votes
1
reply
844
views
Which input data is acceptable for MAST?
SCTransform
MAST
updated 11 months ago by
Andrew_McDavid
▴ 280 • written 11 months ago by
james.watson1
• 0
1
vote
1
reply
695
views
segfault when using singleR with Azimuth reference
SingleR
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Lluís Revilla Sancho
▴ 760
0
votes
1
reply
568
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts
Rsubread
11 months ago
isaac.vock
• 0
0
votes
2
replies
649
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport
DESeq2
updated 11 months ago by
Michael Love
43k • written 11 months ago by
oguzhankaraosmanoglu
• 0
46,630 results • Page
13 of 933
Recent ...
Replies
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
abaed
• 0
Exactly, MDS was computed on logCPM values from `cpm(x, log=TRUE)` after running `calcNormFactors(method="TMMwsp")` on the DGE object. I al…
Answer: GO.db and others package Download failure
by
James W. MacDonald
68k
You didn't get an error. You didn't even get a warning! You simply got a message saying that two (unrelated) packages were not updated. As …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
Gordon Smyth
53k
MDS of what quantity? LogCPM from `cpm()`? I don't have a definitive answer, but my feeling that is that library size effects are to be ex…
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
abaed
• 0
Apologies for not clarifying earlier, you're right: it is a PCA, not an MDS. In local machine, computing the MDS takes quite a long time, P…
Answer: replace cat with message in glmTreat when lfc = 0
by
Gordon Smyth
53k
Yes, I agree that the message should be a `message` rather than `cat` output, and the message is perhaps not needed at all, because anyone …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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